The intuitive way would be to auto focus on the far point and have the value show up and then press the far point in the focus stack (top button), then refocus via AF on the near point and have that value show up and assign it to near point (bottom button) without all of the AF->MF shenanigans.
It seems possible when the tool was designed, using autofocus wasn’t part of the thought process. Despite all the comments here (touch the gear button, make sure the lens actually locks focus before touching the gear button, etc.) the process if trying to use autofocus is too involved and cumbersome and to this point I haven’t been able to use it reliably. To me this is how the steps break down ...
1. Change camera settings so the rear button is not set to AF (in the PODAS workshop I attended the first thing they demonstrated was how to disable AF on the shutter and enable it with the rear button, guessing many photographers use it this way.
2. Perform AF on the near point. You may need to move to MF and AF and back. move to the Focus Stack screen and touch the gear button. The lens may or may not return to the correct point. If it doesn’t, touch the shutter button and acquire focus again, then move back to the FS screen and touch the gear again. Assume eventually you will get the correct point set.
3. Repeat the process again for the far point. Again it may not work correctly so watch the lens closely to insure it is returning to the correct point, then set the far point.
4. Move back to the main screen and lock the mirror up so it doesn’t slap between every exposure.
5. Go back to the FS screen and carefully depress the rear button since timer delay or vibration detect is not honored. There does seem to be some slight delay but it doesn’t seem to be based on the current camera settings or vibration detect ... it may or may not be a long enough delay. It might be advisable to reshoot that particular point from the main screen to insure against camera vibrations from having to physically press this button.
6. Return the camera to your preferred setup.
I think for right now it’s easier just to AF on the near point, compose , throw the camera in manual focus, and gradually rotate the lens to the far point or to infinity.
As it stands the tool is nice for those doing manual focus and live view. When my IQ3 100 comes in, I may find myself using it more often.
It would be nice if the FS tool simply honored all settings in the main capture screen and all buttons function as setup by the user. So move to the FS screen, autofocus the near or far point using whatever button allows this or manual focus with the dials (and a half shutter press doesn’t flip back to the mains screen), set the point, focus the other point, set that point, then trip the sequence by any normal method. Timer delay and vibration detect honored just like from the main screen. Additionally the camera should be smart enough to know the mirror can stay up, and in the case of an LS lens, the FP shutter can stay open (if they engineered this into the new body), so vibrations are minimized.
I’ve sent these ideas to a couple of dealers, other than that I’m not sure how to get feedback to Phase.